In our lab’s most recent paper, we find that most members of stable enrichment communities do not coexist with one another in pairwise coculture, and we also find that competitive exclusion is strongly hierarchical: the most competitive species outcompetes most others, the second most competitive outcompetes most of the ones below (but is oucompeted by the top competitor) and so on.
These two findings can be summarized in a way that I find useful: most bacterial species are driven extinct by the most competitive members of their communities when they face them alone in direct, head-to-head competition. Yet, when the other community members are present too, extinction is avoided and all species coexist stably. As they would say in La Bola de Cristal: “solo no puedes, con amigos sí”. Our study was motivated by a remarkable paper by Jonathan Friedman, Logan Higgins & Jeff Gore. Jonathan and his coworkers took a (semi-random) set of soil bacteria and grew them all in pairwise co-culture under in vitro conditions. They found that the outcome of these bacterial competitions would predict a species presence or absence in more complex assemblages: all species that ended up coexisting together in multispecies communities would also coexist with one another in pairwise coculture. I would want to encourage folks who are not familiar with their paper to go to the source directly and read it. Typical of Jonathan’s papers, this article is beautifully written, rigorous, and thought-provoking, and it prompted us to ask if this additive “rule of assembly” would also work for species that had a prior history of stable coexistence in the same habitat where the pairwise competitions would be carried out. Luckily, in a previous paper we had developed what we thought was an ideal system to address this question, as we had assembled a large number of stable enrichment communities in minimal media with glucose as the only added carbon source. The diversity of these communities is low enough that we could isolate most of their members and compete every pair under the exact same conditions as in their community of origin. We carried out this experiment for 12 of these communities, which contained between 3 and 10 species each, and developed a machine learning approach to quantify the composition of each pairwise co-culture after ~ 60 generations. As summarized above, the additive assembly rule would not have predicted the composition of our experimental communities, and competitive exclusion was the most common outcome. This prompts the question of under what conditions should we expect community assembly to be an emergent property of the community, as opposed to a simple additive affair. What is the main difference between both experiments? Is it the previous history of coexistence under identical culture conditions? Or is it related to growth conditions (nutrients, habitat, buffering, etc)? Are communities assembled from a highly diverse initial pool (as in our own experiments) fundamentally different from those assembled from a low-diversity initial pool (as in Friedman et al)? When additive, pairwise assembly rules fail to predict community composition, is it possible to formulate non-additive pairwise rules that would do the trick? If not, would third-order assembly rules work out, or is it just hopeless? Does the complexity of community assembly reside in the particular network of largely pairwise interactions, or is it the consequence of higher-order interactions between species? There are clearly many open questions that arise from the apparent discrepancy in results between both experiments. Addressing them will benefit from a combination of theoretical models and experiments, and we hope that our study and the tools and model empirical systems we have developed here will be of help in this goal.
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